Molecular methods that provide digital counts of a specific nucleic acid(s) are of interest to the research and clinical community. These methods can be used to discretely measure gene expression (digital gene expression or DGE) or copy number variation (CNV). The precision measurements that can be obtained by digital readouts provides higher confidence in data compared to microarray technology and allows researchers to identify smaller differences between samples or similarly, differences within subsets of cells such as in a tumor biopsy as well as determining cell to cell variations.
However there is still a need for different methods for selective target quantitation that allow for high throughput analysis of transcriptome and genomic regions of interest without specialized instrumentation. The methods, compositions and kits disclosed herein fulfill these needs and provide related advantages.